Contacts of the strand formed by residues 51 - 58 (chain 6) in PDB entry 4N6V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 51 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456 SER* 3.8 13.7 - - - +
466 GLN 3.4 13.2 - - - +
476 VAL* 4.6 12.1 - - + +
486 VAL* 3.9 2.2 - - - +
506 GLY* 1.3 77.0 + - - -
526 ASN* 1.3 72.9 + - - +
536 TYR* 3.6 33.5 + - + +
696 VAL 3.5 1.7 - - - +
706 PHE* 3.6 1.5 - - - -
716 GLN* 2.7 50.5 + - - +
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Residues in contact with ASN 52 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456 SER* 3.2 5.0 - - - -
466 GLN* 2.8 68.4 + - - +
486 VAL* 3.7 18.1 - - - +
516 THR* 1.3 72.8 - - - +
536 TYR* 1.3 61.0 + - - +
546 PHE* 3.8 12.3 - - + -
686 ARG* 3.5 28.8 + - + +
696 VAL 3.3 4.6 + - - +
706 PHE* 3.4 34.1 - - - +
836 SER* 5.0 0.8 + - - -
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Residues in contact with TYR 53 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 GLU* 3.8 16.0 + - - -
166 THR* 6.2 0.7 - - + -
196 ILE* 3.7 31.9 - - + -
436 PHE* 4.1 24.2 - + + -
446 LYS 3.7 1.3 - - - -
456 SER* 4.1 15.5 - - - -
516 THR* 3.6 28.4 + - + +
526 ASN* 1.3 72.2 - - - +
546 PHE* 1.3 61.2 + - - +
556 ILE* 4.0 18.8 + - + -
676 LEU 3.4 1.4 - - - +
686 ARG* 3.3 4.0 - - - -
696 VAL* 2.8 46.7 + - + +
716 GLN* 3.4 41.4 + - + -
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Residues in contact with PHE 54 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436 PHE* 3.0 6.8 - - - +
446 LYS* 2.8 47.9 + - + +
466 GLN* 3.6 26.7 - - - -
526 ASN* 3.8 14.6 - - + -
536 TYR* 1.3 75.1 - - - +
556 ILE* 1.3 59.4 + - - +
676 LEU 3.1 4.5 - - - +
686 ARG* 3.6 28.9 - - + -
956 LEU* 3.3 14.5 - - + +
966 THR 4.2 1.6 - - - +
976 TYR* 3.3 38.4 - + + -
986 PHE* 3.3 57.0 - + - -
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Residues in contact with ILE 55 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166 THR* 3.8 18.8 - - + +
196 ILE* 3.7 31.2 - - + -
206 ALA* 4.1 9.4 - - + +
406 ALA* 3.8 20.4 - - + -
426 SER 3.4 9.9 - - - +
436 PHE* 4.2 7.2 - - + -
536 TYR* 4.1 17.3 - - + +
546 PHE* 1.3 78.4 - - - +
566 LYS* 1.3 63.6 + - - +
576 VAL* 3.6 22.4 + - + +
656 VAL 3.5 1.2 - - - +
666 HIS* 3.2 3.3 - - - -
676 LEU* 2.8 41.9 + - + +
696 VAL* 4.5 7.6 - - + -
956 LEU* 4.0 5.0 - - - +
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Residues in contact with LYS 56 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406 ALA* 3.6 2.9 - - - -
416 VAL* 2.9 41.9 + - + +
426 SER* 2.9 31.5 + - - +
556 ILE* 1.3 71.3 - - - +
576 VAL* 1.3 62.2 + - - +
646 PHE* 3.9 20.4 - - + +
656 VAL 3.7 3.1 - - - -
666 HIS* 2.9 34.7 + - + +
896 LYS* 4.5 0.2 - - - +
906 ALA 2.8 29.1 + - - -
916 LYS* 3.6 16.8 - - - +
936 ASP* 2.8 24.2 + - - +
956 LEU* 3.8 11.2 - - + +
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Residues in contact with VAL 57 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206 ALA* 4.4 4.9 - - + -
386 PHE* 3.6 33.4 - - + +
396 LYS 3.4 24.7 - - - +
406 ALA* 4.2 3.8 - - - +
556 ILE* 3.6 24.0 - - + +
566 LYS* 1.3 78.7 - - - +
586 HIS* 1.3 67.6 + - - +
596 VAL* 3.8 3.0 - - + +
646 PHE* 3.2 8.6 - - - -
656 VAL* 2.9 39.4 + - + +
676 LEU* 3.8 25.4 - - + -
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Residues in contact with HIS 58 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376 VAL* 3.4 20.7 - - + +
386 PHE* 3.3 8.7 + - - -
396 LYS* 2.8 50.8 + - + +
416 VAL* 4.6 5.1 - - + +
566 LYS 4.3 0.2 - - - -
576 VAL* 1.3 71.0 - - - +
596 VAL* 1.3 57.8 + - - +
606 GLY* 3.3 20.3 + - - -
616 ASP 3.9 2.0 + - - -
626 GLU* 3.1 35.7 - - + -
636 ASP 3.2 10.3 + - - -
646 PHE* 3.4 30.9 - + + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il